Theory for RNA folding, stretching, and melting including loops and salt. (arXiv:1104.4129v1 [physics.bio-ph])

Secondary structure formation of nucleic acids strongly depends on salt
concentration and temperature. We develop a theory for RNA folding that
correctly accounts for sequence effects, the entropic contributions associated
with loop formation, and salt effects. Using an iterative expression for the
partition function that neglects pseudoknots, we calculate folding free
energies and minimum free energy configurations based on the experimentally
derived base pairing free energies. The configurational entropy of loop
formation is modeled by the asymptotic expression -c ln m, where m is the
length of the loop and c the loop exponent, which is an adjustable constant.
Salt effects enter in two ways: first, we derive salt induced modifications of
the free energy parameters for describing base pairing and, second, we include
the electrostatic free energy for loop formation. Both effects are modeled on
the Debye-Hueckel level including counterion condensation. We validate our
theory for two different RNA sequences: For tRNA-phe, the resultant heat
capacity curves for thermal denaturation at various salt concentrations
accurately reproduce experimental results. For the P5ab RNA hairpin, we derive
the global phase diagram in the three-dimensional space spanned by temperature,
stretching force, and salt concentration and obtain good agreement with the
experimentally determined critical unfolding force. We show that for a proper
description of RNA melting and stretching, both salt and loop entropy effects
are needed.

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